Silver in PDB 8gk2: Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide

The structure of Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide, PDB code: 8gk2 was solved by S.S.Hess, A.I.Nguyen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.72 / 0.89
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	8.449, 16.716, 55.087, 90, 90, 90
R / Rfree (%)	17.2 / 20

The binding sites of Silver atom in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide (pdb code 8gk2). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 5 binding sites of Silver where determined in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide, PDB code: 8gk2:
Jump to Silver binding site number: 1; 2; 3; 4; 5;

Silver binding site 1 out of 5 in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:8.7 occ:1.00 SG A:CYS8 2.4 7.4 1.0 O A:HOH203 2.5 7.8 1.0 HB12 A:AIB9 2.6 5.6 1.0 O A:CYS8 2.7 4.2 1.0 AG A:AG105 3.1 21.9 1.0 C A:CYS8 3.2 4.2 1.0 CB1 A:AIB9 3.5 4.6 1.0 HB13 A:AIB9 3.6 5.6 1.0 CB A:CYS8 3.7 5.9 1.0 HA A:CYS8 3.7 6.3 1.0 CA A:CYS8 3.7 5.2 1.0 N A:AIB9 3.9 4.1 1.0 HB3 A:CYS8 4.1 7.2 1.0 H1 A:I77102 4.2 4.2 0.2 CA A:AIB9 4.3 4.3 1.0 AG A:AG106 4.3 26.5 1.0 HB11 A:AIB9 4.3 5.6 1.0 H A:AIB9 4.4 5.0 0.5 HB2 A:CYS8 4.4 7.2 1.0 H1 A:I77102 4.4 6.8 0.8 C A:AIB9 4.8 4.0 1.0 O A:AIB9 4.9 4.6 1.0

Silver binding site 2 out of 5 in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:21.9 occ:1.00 SG A:CYS8 2.4 7.4 1.0 HA A:CYS8 3.1 6.3 1.0 AG A:AG104 3.1 8.7 1.0 CB A:CYS8 3.3 5.9 1.0 HB2 A:CYS8 3.3 7.2 1.0 AG A:AG106 3.4 26.5 1.0 CA A:CYS8 3.6 5.2 1.0 O A:CYS8 4.1 4.2 1.0 HB3 A:CYS8 4.2 7.2 1.0 C A:CYS8 4.3 4.2 1.0 O2 A:NO3103 4.5 24.6 1.0 N A:CYS8 4.9 4.8 1.0 H111 A:I77102 4.9 8.1 0.8 H171 A:I77102 4.9 3.6 0.2

Silver binding site 3 out of 5 in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:26.5 occ:1.00 SG A:CYS8 2.3 7.4 1.0 O1 A:NO3103 2.9 22.2 1.0 O2 A:NO3103 3.1 24.6 1.0 N A:NO3103 3.3 23.1 1.0 HB2 A:CYS8 3.3 7.2 1.0 AG A:AG105 3.4 21.9 1.0 CB A:CYS8 3.4 5.9 1.0 HB3 A:CYS8 3.7 7.2 1.0 O3 A:NO3103 4.3 22.4 1.0 AG A:AG104 4.3 8.7 1.0 O A:HOH203 4.7 7.8 1.0 CA A:CYS8 4.8 5.2 1.0 HA A:CYS8 4.9 6.3 1.0

Silver binding site 4 out of 5 in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:11.3 occ:0.72 H051 A:I77102 1.3 6.9 0.8 H181 A:I77102 1.5 8.5 0.8 C05 A:I77102 2.3 5.6 0.8 C18 A:I77102 2.3 7.0 0.8 N10 A:I77102 2.4 3.7 0.2 N07 A:I77102 2.6 3.0 0.2 C09 A:I77102 3.1 7.0 0.8 C08 A:I77102 3.1 6.2 0.8 H111 A:I77102 3.1 4.2 0.2 C11 A:I77102 3.2 3.4 0.2 C04 A:I77102 3.3 6.2 0.8 C17 A:I77102 3.3 7.3 0.8 C09 A:I77102 3.3 4.1 0.2 H061 A:I77102 3.4 5.4 0.2 C08 A:I77102 3.4 4.1 0.2 C06 A:I77102 3.4 4.4 0.2 H041 A:I77102 3.4 7.5 0.8 H171 A:I77102 3.5 8.9 0.8 N10 A:I77102 4.3 7.2 0.8 N07 A:I77102 4.3 7.1 0.8 C12 A:I77102 4.5 2.6 0.2 C03 A:I77102 4.5 6.7 0.8 C12 A:I77102 4.5 5.3 0.8 C18 A:I77102 4.6 4.0 0.2 C05 A:I77102 4.7 5.5 0.2 C03 A:I77102 4.7 5.7 0.2 C11 A:I77102 4.9 6.6 0.8 C06 A:I77102 4.9 7.0 0.8

Silver binding site 5 out of 5 in the Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Porous Framework Formed By Assembly of A Bipyridyl-Conjugated Helical Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:12.6 occ:0.28 H181 A:I77102 1.1 4.9 0.2 H051 A:I77102 1.4 6.7 0.2 C18 A:I77102 1.9 4.0 0.2 C05 A:I77102 2.2 5.5 0.2 N07 A:I77102 2.3 7.1 0.8 N10 A:I77102 2.3 7.2 0.8 C09 A:I77102 2.6 4.1 0.2 C08 A:I77102 2.7 4.1 0.2 C09 A:I77102 2.9 7.0 0.8 C08 A:I77102 3.0 6.2 0.8 C17 A:I77102 3.1 3.0 0.2 C11 A:I77102 3.3 6.6 0.8 C06 A:I77102 3.3 7.0 0.8 H171 A:I77102 3.4 3.6 0.2 C04 A:I77102 3.4 6.0 0.2 H061 A:I77102 3.5 8.5 0.8 H111 A:I77102 3.5 8.1 0.8 H041 A:I77102 3.8 7.3 0.2 N10 A:I77102 3.8 3.7 0.2 N07 A:I77102 4.1 3.0 0.2 C18 A:I77102 4.2 7.0 0.8 C12 A:I77102 4.2 2.6 0.2 C05 A:I77102 4.3 5.6 0.8 C12 A:I77102 4.5 5.3 0.8 C11 A:I77102 4.5 3.4 0.2 C03 A:I77102 4.6 5.7 0.2 C03 A:I77102 4.6 6.7 0.8 C06 A:I77102 4.8 4.4 0.2 C17 A:I77102 4.9 7.3 0.8 H181 A:I77102 4.9 8.5 0.8

S.S.Hess, F.Coppola, V.T.Dang, P.N.Tran, P.J.Mickel, J.Oktawiec, Z.Ren, P.Kral, A.I.Nguyen. Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. J.Am.Chem.Soc. V. 145 19588 2023.
ISSN: ESSN 1520-5126
PubMed: 37639365
DOI: 10.1021/JACS.3C03645